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What are the functional properties of new mutations and how do they influence which mutations segregate within a species and become fixed between species?

Regulatory variation within and between species reflects the interplay of mutation, selection, and drift. Distinguishing the relative roles of these forces is complicated by our ignorance of even basic functional properties of new mutations. To better understand the mutational processes that create regulatory variation, we developed a powerful experimental system that uses the baker’s yeast Saccharomyces cerevisiae to isolate and characterize hundreds of novel genotypes with altered expression of a focal gene, each containing a new regulatory mutation (Gruber et al. 2012).

Thus far, we have measured the relative frequency, effects, and dominance of 231 coding, cis-regulatory, trans-regulatory, and copy number mutants affecting activity of a reporter gene driven by the S. cerevisiae TDH3 promoter. We found differences in all three of these properties among functional classes (frequency and effects shown in Figure). For example, mutations that altered reporter gene activity by changing its regulation were more than 10 times more common than mutations that altered its activity by changing the protein sequence encoded by the reporter gene, suggesting that regulatory changes are the most abundant source of variation in a gene’s activity.

Furthermore, regulatory mutations had moremoderate effects on gene activity, suggesting that they might have more subtle effects on phenotypes than coding mutations. Finally, trans-regulatory mutations were much more common than cis-regulatory mutations (187 trans vs 4 cis recovered) and also much more likely to be recessive (data not shown). This high mutation rate and recessivity might maintain a large pool of segregating trans-regulatory variants, helping to explain the excess of trans-regulatory variation observed within relative to between species (Wittkopp et al. 2008; Emerson et al. 2010).

Currently, we are (1) mapping the trans-acting mutations recovered to determine how they are distributed within the regulatory network, (2) expanding the collection of cis-regulatory mutations for this gene, (3) comparing the mutational spectrum recovered for this gene to variants segregating in natural populations, and (4) completing similar analysis for other genes to assess the generality of the patterns observed.